1BGO

CRYSTAL STRUCTURE OF CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT PEPTIDOMIMETIC INHIBITOR

PDB DOI: https://doi.org/10.2210/pdb1BGO/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 1998-05-29 Released: 1999-06-08
Deposition Author(s): Desjarlais, R.L., Yamashita, D.S., Oh, H.-J., Bondinell, W.E., Uzinskas, I.N., Erhard, K.F., Allen, A.C., Haltiwanger, R.C., Zhao, B., Smith, W.W., Abdel-Meguid, S.S., D'Alessio, K., Janson, C.A., Mcqueney, M.S., Tomaszek, T.A., Levy, M.A., Veber, D.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.296
R-Value Work: 0.240
R-Value Observed: 0.240

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Use of X-Ray Co-Crystal Structures and Molecular Modeling to Design Potent and Selective Non-Peptide Inhibitors of Cathepsin K

Desjarlais, R.L., Yamashita, D.S., Oh, H.J., Uzinskas, I.N., Erhard, K.F., Allen, A.C., Haltiwanger, R.C., Zhao, B.G., Smith, W.W., Abdel-Meguid, S.S., Dalessio, K., Janson, C.A., Mcqueney, M.S., Tomaszek, T.A., Levy, M.A., Veber, D.F.

(1998) J Am Chem Soc 120: 9114

Macromolecule Content

Total Structure Weight: 24.01 kDa
Atom Count: 1,702
Modelled Residue Count: 215
Deposited Residue Count: 215
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATHEPSIN K	A	215	Homo sapiens	Mutation(s): 0 EC: 3.4.22.38
UniProt & NIH Common Fund Data Resources
Find proteins for P43235 (Homo sapiens) Explore P43235 Go to UniProtKB: P43235
PHAROS: P43235 GTEx: ENSG00000143387
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43235
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
I10 Query on I10 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1-[2-(3-BIPHENYL)-4-METHYLVALERYL)]AMINO-3-(2-PYRIDYLSULFONYL)AMINO-2-PROPANONE C₂₆ H₃₁ N₃ O₄ S YCDHZDINQZLSRR-DNQXCXABSA-N		Interactions Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
I10	PDBBind: 1BGO	Ki: 3.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.296
R-Value Work: 0.240
R-Value Observed: 0.240
Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.55	α = 90
b = 71.55	β = 90
c = 55.09	γ = 90

Software Package:

Software Name	Purpose
XENGEN	data collection
CCP4	data reduction
X-PLOR	model building
X-PLOR	refinement
XENGEN	data reduction
CCP4	data scaling
X-PLOR	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1999-06-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1999-06-08
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-03-07
Changes: Data collection, Other
Version 1.4: 2023-08-02
Changes: Database references, Derived calculations, Refinement description
Version 1.5: 2024-10-23
Changes: Data collection, Structure summary